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I noticed this whenever you sign a treaty in regular Alpha Centauri, but I was under the impression that the Progenitors were added in the expansion.

So, I'm guessing this is leftover from an unused feature or something. (Like the chi waves in System Shock)
Also reported here. This phrase ("Treaties and pacts with Progenitor factions have no effect on Commerce.") comes from the file tutor.txt and is triggered if you have enabled tutorial messages in MENU --> GAME --> Preferences. Just a guess, but GOG may have used the most recent version of tutor.txt (created after the release of Alien Crossfire), instead of using a prior version. You also can find references to the Progenitors in the file script.txt (which provides the text for many popup dialogs).
Also note that the original game made many references to things only added in the expansion pack long before it was even formally announced, so it seemed they had planned for it all along. Off the top of my head, I can remember references to the Cult of Planet and fungal towers, even though neither was actually in the game until the expansion.
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catwhowalks: Also note that the original game made many references to things only added in the expansion pack long before it was even formally announced, so it seemed they had planned for it all along. Off the top of my head, I can remember references to the Cult of Planet and fungal towers, even though neither was actually in the game until the expansion.
Just out of raw curiosity, do you have examples of where exactly this phenomenon happened? I'm quite dearly interested. It would be quite interesting details to record down.
The reference to Cult of Planet and fungal towers is in the "Interludes from Book of Planet" you get when you begin building the Ascent to Transcendence.
Ahh, I see now! Thanks a lot, mate!